BLASTP 2.2.26 [Sep-21-2011]


Reference: Altschul, Stephen F., Thomas L. Madden, Alejandro A. Schaffer, 
Jinghui Zhang, Zheng Zhang, Webb Miller, and David J. Lipman (1997), 
"Gapped BLAST and PSI-BLAST: a new generation of protein database search
programs",  Nucleic Acids Res. 25:3389-3402.


Reference for compositional score matrix adjustment: Altschul, Stephen F., 
John C. Wootton, E. Michael Gertz, Richa Agarwala, Aleksandr Morgulis,
Alejandro A. Schaffer, and Yi-Kuo Yu (2005) "Protein database searches
using compositionally adjusted substitution matrices", FEBS J. 272:5101-5109.

Query= psy424
         (98 letters)

Database: pdbaa 
           62,578 sequences; 14,973,337 total letters

Searching..................................................done



>pdb|2WWB|C Chain C, Cryo-Em Structure Of The Mammalian Sec61 Complex Bound
          To The Actively Translating Wheat Germ 80s Ribosome
          Length = 96

 Score =  115 bits (288), Expect = 7e-27,   Method: Compositional matrix adjust.
 Identities = 64/95 (67%), Positives = 71/95 (74%), Gaps = 3/95 (3%)

Query: 3  PAPASSTSVGSGTRSPKAGGPGGRPTGSTVRQRKPTTTTAARSNRT-GAGSGGMWRYYTD 61
          P P S T+VGS  RSP       R  GSTVRQRK  +     + RT  AG+GGMWR+YT+
Sbjct: 4  PTP-SGTNVGSSGRSPSKA-VAARAAGSTVRQRKNASCGTRSAGRTTSAGTGGMWRFYTE 61

Query: 62 DSPGIKVGPVPVLVMSLLFIASVFMLHIWGKYTRS 96
          DSPG+KVGPVPVLVMSLLFIASVFMLHIWGKYTRS
Sbjct: 62 DSPGLKVGPVPVLVMSLLFIASVFMLHIWGKYTRS 96


>pdb|2WW9|C Chain C, Cryo-Em Structure Of The Active Yeast Ssh1 Complex Bound
          To The Yeast 80s Ribosome
 pdb|2WWA|C Chain C, Cryo-Em Structure Of Idle Yeast Ssh1 Complex Bound To
          The Yeast 80s Ribosome
          Length = 87

 Score = 45.1 bits (105), Expect = 1e-05,   Method: Compositional matrix adjust.
 Identities = 25/80 (31%), Positives = 42/80 (52%), Gaps = 7/80 (8%)

Query: 23 PGG------RPTGSTVRQRKPTTT-TAARSNRTGAGSGGMWRYYTDDSPGIKVGPVPVLV 75
          PGG      R    ++++++   T T+ R    G  S  + + YTD++ G +V  + VL 
Sbjct: 7  PGGQRILQKRRQAQSIKEKQAKQTPTSTRQAGYGGSSSSILKLYTDEANGFRVDSLVVLF 66

Query: 76 MSLLFIASVFMLHIWGKYTR 95
          +S+ FI SV  LH+  K+T 
Sbjct: 67 LSVGFIFSVIALHLLTKFTH 86


>pdb|4FT2|A Chain A, Crystal Structure Of Zea Mays Zmet2 In Complex
           H3(1-15)k9me2 Peptide And Sah
 pdb|4FT2|B Chain B, Crystal Structure Of Zea Mays Zmet2 In Complex
           H3(1-15)k9me2 Peptide And Sah
 pdb|4FT4|B Chain B, Crystal Structure Of Zea Mays Zmet2 In Complex
           H3(1-32)k9me2 Peptide And Sah
 pdb|4FT4|A Chain A, Crystal Structure Of Zea Mays Zmet2 In Complex
           H3(1-32)k9me2 Peptide And Sah
          Length = 784

 Score = 25.8 bits (55), Expect = 5.7,   Method: Composition-based stats.
 Identities = 13/30 (43%), Positives = 13/30 (43%)

Query: 5   PASSTSVGSGTRSPKAGGPGGRPTGSTVRQ 34
           P S TSVG  T       P G P G  V Q
Sbjct: 755 PPSFTSVGGRTAGQARASPVGTPAGEVVEQ 784


>pdb|4FSX|A Chain A, Crystal Structure Of Se-Substituted Zea Mays Zmet2 In
           Complex With Sah
 pdb|4FSX|B Chain B, Crystal Structure Of Se-Substituted Zea Mays Zmet2 In
           Complex With Sah
          Length = 784

 Score = 25.8 bits (55), Expect = 5.8,   Method: Composition-based stats.
 Identities = 13/30 (43%), Positives = 13/30 (43%)

Query: 5   PASSTSVGSGTRSPKAGGPGGRPTGSTVRQ 34
           P S TSVG  T       P G P G  V Q
Sbjct: 755 PPSFTSVGGRTAGQARASPVGTPAGEVVEQ 784


  Database: pdbaa
    Posted date:  Mar 3, 2013 10:34 PM
  Number of letters in database: 14,973,337
  Number of sequences in database:  62,578
  
Lambda     K      H
   0.313    0.129    0.392 

Lambda     K      H
   0.267   0.0410    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 3,255,396
Number of Sequences: 62578
Number of extensions: 131306
Number of successful extensions: 147
Number of sequences better than 100.0: 13
Number of HSP's better than 100.0 without gapping: 10
Number of HSP's successfully gapped in prelim test: 3
Number of HSP's that attempted gapping in prelim test: 136
Number of HSP's gapped (non-prelim): 14
length of query: 98
length of database: 14,973,337
effective HSP length: 64
effective length of query: 34
effective length of database: 10,968,345
effective search space: 372923730
effective search space used: 372923730
T: 11
A: 40
X1: 16 ( 7.2 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 42 (21.9 bits)
S2: 45 (21.9 bits)